Most people will go with Shredder, but I have to say Mr. Null. He is responsible for having Mondo Gecko, Leatherhead, Wingnut, Screwloose, Jagwar, Dreadmon, and Ray Fillet killed after all. Plus he looks more like the devil everytime he does something evil, and in his last comic book appearance he had huge horns, bat wings, and a pointy tail so you be the judge.
Most evil TMNT villain
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